Hello,
I have two subunits (let say alpha and beta) between them a linker sequence (29 amino acid). I have modeled the alpha and beta subunit using templates extracted from PDB. There is no homologous structure in the PDB with the linker sequence. So, I have modeled the loop using LOMETS server (I-tasser). when I used the linker and both subunits structures as a template to model the structure containing linker and both subunits. After analysis, i see some weird conformation of loop joining both subunits, linker passing within the subunits to join the terminal of subunits. How can I merge both subunits by inputting the linker between them in a proper way?
Make two sub-units and merge them through Photoshop :D
hahaha
just kidding.....
brother, after that iI have to do simulation followed by validation through experiments
Hello,
You just develop the linker loop in some modeling application like MOE, Chimera etc, and put peptide bonds of both the termini and their corresponding terminal of the subunit protein. Subsequently, subject your complex to short md simulation to make it refined and to remove any bad contact. The validation of your complex and the appearance of the inserted loop will let you decide whether your complex is correct or not.
Good luck
Dear @Amir zeb,
Both the terminal are apart from each other, so how can I join both terminal with short linker? how to do in chimera?
By using protein-protein docking software, you can bring two subunits close enough for linker generation. Next, you rename the chain ID of subunits as A. Then you can perform a regular homology modeling to "fuse" two subunits and generate the linker structure. Of course, you need to do MD in order to optimize the whole conformation.
thanks @Jyung-Hurng Liu and @Aditi Gangopadhyay for your valuable suggestions
I have solved this problem in the following way as suggested in the comment.
1. First model the linker in MOE software
2. then merged linker with both subunit in a right way
3. then jioned the peptide bond of the linker with subunit follwed by MD simulation
Aditis Gangopadhyay is right. MODELLER is a good option for loop optimization task. Additionally, MODELLER is free and MOE is not.
We did this a few years back, but you can look in the methods section of this paper http://www.sciencedirect.com/science/article/pii/S0168165612003495
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